http://www.cnblogs.com/davidluozw/archive/2008/02/15/1069223.html
This is a new feature added in SP 2010 and VS supports this.
You can add the files to the webpart in your project and open the properties window. With the file selected, set the deploymentType = AppGlobalResources. This will package the file correctly to be deployed to App_GlobalResources everytime you Deploy.